SMTL ID : 5mjs.1

S. pombe microtubule copolymerized with GTP and Mal3-143

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-4-mer

Ligands

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 17 residues within 4Å: Chain A: G.10, Q.11, C.12, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, D.177, N.204, Y.222, N.226 Chain D: L.252 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:S.138, A:G.140, A:G.142, A:T.143, A:T.143, A:T.143, A:G.144, A:S.145, A:D.177, A:N.204, A:N.226, A:N.226, A:N.226 pi-Stacking: A:Y.222 GDP.6: 17 residues within 4Å: Chain C: L.252 Chain G: G.10, Q.11, C.12, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, D.177, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:Q.11, G:C.12, G:S.138, G:G.140, G:G.142, G:T.143, G:T.143, G:T.143, G:G.144, G:S.145, G:D.177, G:N.204, G:N.226, G:N.226, G:N.226 pi-Stacking: G:Y.222 GDP.7: 16 residues within 4Å: Chain H: G.10, Q.11, C.12, V.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, D.177, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:S.138, H:G.140, H:G.142, H:T.143, H:T.143, H:T.143, H:G.144, H:S.145, H:D.177, H:N.204, H:N.226, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 GDP.8: 16 residues within 4Å: Chain I: G.10, Q.11, C.12, V.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, D.177, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:Q.11, I:C.12, I:S.138, I:G.140, I:G.142, I:T.143, I:T.143, I:T.143, I:G.144, I:S.145, I:D.177, I:N.204, I:N.226, I:N.226, I:N.226 pi-Stacking: I:Y.222, I:Y.222

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 20 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.73, D.102, S.104, N.105, S.144, G.146, G.147, G.148, T.149, G.150, T.183, E.187, N.210, Y.228, N.232 Chain H: L.246 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:Q.15, C:Q.15, C:S.104, C:N.105, C:S.144, C:G.146, C:G.148, C:T.149, C:T.149, C:T.149, C:T.149, C:G.150, C:T.183, C:T.183, C:E.187, C:N.210, C:N.232 pi-Cation interactions: C:Y.228 GTP.3: 20 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, D.73, D.102, S.104, N.105, S.144, G.146, G.147, G.148, T.149, G.150, T.183, E.187, N.210, Y.228, N.232 Chain I: L.246 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:Q.15, D:Q.15, D:S.104, D:S.104, D:N.105, D:S.144, D:G.146, D:G.148, D:T.149, D:T.149, D:T.149, D:T.149, D:G.150, D:T.183, D:T.183, D:E.187, D:N.210, D:N.232 pi-Cation interactions: D:Y.228 GTP.4: 20 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.73, D.102, S.104, N.105, S.144, G.146, G.147, G.148, T.149, G.150, T.183, E.187, N.210, Y.228, N.232 Chain G: L.246 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:Q.11, E:Q.11, E:Q.15, E:Q.15, E:S.104, E:S.104, E:N.105, E:S.144, E:G.146, E:G.148, E:T.149, E:T.149, E:T.149, E:T.149, E:G.150, E:T.183, E:T.183, E:E.187, E:N.210, E:N.232 pi-Cation interactions: E:Y.228 GTP.5: 20 residues within 4Å: Chain A: L.246 Chain F: G.10, Q.11, A.12, Q.15, D.73, D.102, S.104, N.105, S.144, G.146, G.147, G.148, T.149, G.150, T.183, E.187, N.210, Y.228, N.232 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:Q.15, F:Q.15, F:S.104, F:N.105, F:S.144, F:G.146, F:G.148, F:T.149, F:T.149, F:T.149, F:T.149, F:G.150, F:T.183, F:T.183, F:E.187, F:N.210, F:N.232 pi-Cation interactions: F:Y.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

von Loeffelholz, O. et al., Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics. Nat Commun (2017)

Release Date

2017-12-20

Peptides

Tubulin beta chain: AGHI
Microtubule integrity protein mal3: B
Tubulin alpha-1 chain: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
J

H
B

I
C

B
D

C
E

D
F

E
G

F
H

Tubulin beta chain

Microtubule integrity protein mal3

Tubulin alpha-1 chain